Buggy code:
public class SetClasspathOperation extends JavaModelOperation { IClasspathEntry [ ] oldResolvedPath ; IClasspathEntry [ ] newRawPath ; boolean canChangeResource ; boolean needCycleCheck ; boolean needValidation ; IPath newOutputLocation ; public static final IClasspathEntry [ ] ReuseClasspath = new IClasspathEntry [ 0 ] ; public static final IPath ReuseOutputLocation = new Path ( "Reuse<seq2seq4repair_space>Existing<seq2seq4repair_space>Output<seq2seq4repair_space>Location" ) ; public SetClasspathOperation ( IJavaProject project , IClasspathEntry [ ] oldResolvedPath , IClasspathEntry [ ] newRawPath , IPath newOutputLocation , boolean canChangeResource , boolean forceSave , boolean needCycleCheck , boolean needValidation ) { } protected void addClasspathDeltas ( IPackageFragmentRoot [ ] roots , int flag , JavaElementDelta delta ) { } protected int classpathContains ( IClasspathEntry [ ] list , IClasspathEntry entry ) { } protected void collectAllSubfolders ( IFolder folder , ArrayList collection ) throws JavaModelException { } protected ArrayList determineAffectedPackageFragments ( IPath location ) throws JavaModelException { } protected void executeOperation ( ) throws JavaModelException { } protected void generateClasspathChangeDeltas ( IClasspathEntry [ ] oldResolvedPath , IClasspathEntry [ ] newResolvedPath , JavaModelManager manager , JavaProject project ) { boolean needToUpdateDependents = false ; JavaElementDelta delta = new JavaElementDelta ( getJavaModel ( ) ) ; boolean hasDelta = false ; int oldLength = oldResolvedPath . length ; int newLength = newResolvedPath . length ; boolean oldResolvedPathLongest = oldLength >= newLength ; IndexManager indexManager = manager . getIndexManager ( ) ; for ( int i = 0 ; i < ( oldResolvedPath . length ) ; i ++ ) { int index = classpathContains ( newResolvedPath , oldResolvedPath [ i ] ) ; if ( index == ( - 1 ) ) { if ( ( oldResolvedPath [ i ] . getEntryKind ( ) ) == ( IClasspathEntry . CPE_PROJECT ) ) { needToUpdateDependents = true ; continue ; } IPackageFragmentRoot [ ] pkgFragmentRoots = project . getPackageFragmentRoots ( oldResolvedPath [ i ] ) ; addClasspathDeltas ( pkgFragmentRoots , IJavaElementDelta . F_REMOVED_FROM_CLASSPATH , delta ) ; int changeKind = oldResolvedPath [ i ] . getEntryKind ( ) ; needToUpdateDependents |= ( changeKind == ( IClasspathEntry . CPE_SOURCE ) ) || ( oldResolvedPath [ i ] . isExported ( ) ) ; if ( ( indexManager != null ) && ( changeKind == ( IClasspathEntry . CPE_SOURCE ) ) ) { indexManager . removeSourceFolderFromIndex ( project , oldResolvedPath [ i ] . getPath ( ) ) ; } hasDelta = true ; } else { if ( ( oldResolvedPath [ i ] . getEntryKind ( ) ) == ( IClasspathEntry . CPE_PROJECT ) ) { continue ; } needToUpdateDependents |= ( oldResolvedPath [ i ] . isExported ( ) ) != ( newResolvedPath [ index ] . isExported ( ) ) ; if ( oldResolvedPathLongest && ( index != i ) ) { addClasspathDeltas ( project . getPackageFragmentRoots ( oldResolvedPath [ i ] ) , IJavaElementDelta . F_CLASSPATH_REORDER , delta ) ; int changeKind = oldResolvedPath [ i ] . getEntryKind ( ) ; needToUpdateDependents |= changeKind == ( IClasspathEntry . CPE_SOURCE ) ; hasDelta = true ; } int sourceAttachmentFlags = this . getSourceAttachmentDeltaFlag ( oldResolvedPath [ i ] . getSourceAttachmentPath ( ) , newResolvedPath [ index ] . getSourceAttachmentPath ( ) ) ; int sourceAttachmentRootFlags = this . getSourceAttachmentDeltaFlag ( oldResolvedPath [ i ] . getSourceAttachmentRootPath ( ) , newResolvedPath [ index ] . getSourceAttachmentRootPath ( ) ) ; int flags = sourceAttachmentFlags | sourceAttachmentRootFlags ; if ( flags != 0 ) { <START_BUG> addClasspathDeltas ( project . getPackageFragmentRoots ( oldResolvedPath [ i ] ) , ( flags | ( IJavaElementDelta . F_REMOVED_FROM_CLASSPATH ) ) , delta ) ; <END_BUG> hasDelta = true ; } } } for ( int i = 0 ; i < ( newResolvedPath . length ) ; i ++ ) { int index = classpathContains ( oldResolvedPath , newResolvedPath [ i ] ) ; if ( index == ( - 1 ) ) { if ( ( newResolvedPath [ i ] . getEntryKind ( ) ) == ( IClasspathEntry . CPE_PROJECT ) ) { needToUpdateDependents = true ; continue ; } addClasspathDeltas ( project . getPackageFragmentRoots ( newResolvedPath [ i ] ) , IJavaElementDelta . F_ADDED_TO_CLASSPATH , delta ) ; int changeKind = newResolvedPath [ i ] . getEntryKind ( ) ; if ( indexManager != null ) { switch ( changeKind ) { case IClasspathEntry . CPE_LIBRARY : boolean pathHasChanged = true ; IPath newPath = newResolvedPath [ i ] . getPath ( ) ; for ( int j = 0 ; j < ( oldResolvedPath . length ) ; j ++ ) { IClasspathEntry oldEntry = oldResolvedPath [ j ] ; if ( oldEntry . getPath ( ) . equals ( newPath ) ) { pathHasChanged = false ; break ; } } if ( pathHasChanged ) { indexManager . indexLibrary ( newPath , project . getProject ( ) ) ; } break ; case IClasspathEntry . CPE_SOURCE : indexManager . indexSourceFolder ( project , newResolvedPath [ i ] . getPath ( ) ) ; break ; } } needToUpdateDependents |= ( changeKind == ( IClasspathEntry . CPE_SOURCE ) ) || ( newResolvedPath [ i ] . isExported ( ) ) ; hasDelta = true ; } } if ( hasDelta ) { this . addDelta ( delta ) ; } if ( needToUpdateDependents ) { updateAffectedProjects ( project . getProject ( ) . getFullPath ( ) ) ; } } protected JavaProject getProject ( ) { } private int getSourceAttachmentDeltaFlag ( IPath oldPath , IPath newPath ) { } public boolean isReadOnly ( ) { } protected void saveClasspathIfNecessary ( ) throws JavaModelException { } public String toString ( ) { } private void updateClasspath ( ) throws JavaModelException { } protected void updateAffectedProjects ( IPath prerequisiteProjectPath ) { } protected void updateCycleMarkers ( IClasspathEntry [ ] newResolvedPath ) { } protected void updateOutputLocation ( ) throws JavaModelException { } protected void updateProjectReferencesIfNecessary ( ) throws JavaModelException { } public IJavaModelStatus verify ( ) { } }

Fix:
addClasspathDeltas ( project . getPackageFragmentRoots ( oldResolvedPath [ i ] ) , flags , delta ) ;